Baumwelch iteration Maximization Step cannot complete after 200 rounds causing msmc exits with error

[zhoujinjean]

Hi,

Can anyone help me with this issue?

I am running MSMC on chr1 sequencing data of 4 individuals (two individual from one population). Therefore, I have eight haploid sequences in total. I prepared the input file following the pipeline provided by msmc paper.

The command I used to run is: msmc_linux_64bit --fixedRecombination --skipAmbiguous -P 0,0,0,0,1,1,1,1 -o output input

However, the program exits without giving me a output.final.txt. I checked the log file and found that the Baumwelch iteration' Maximization Step cannot complete after 200 rounds. The log file ends with:

^M * [186/200(max)] Maximization Step^M * [187/200(max)] Maximization Step^M * [188/200(max)] Maximization Step^M * [189/200(max)] Maximization Step^M * [190/200(max)] Maximization Step^M * [191/200(max)] Maximization Step^M * [192/200(max)] Maximization Step^M^M * [193/200(max)] Maximization Step^M * [194/200(max)] Maximization Step^M * [195/200(max)] Maximization Step^M * [196/200(max)] Maximization Step^M * [197/200(max)] Maximization Step^M * [198/200(max)] Maximization Step^M * [199/200(max)] Maximization Step^M^M * [200/200(max)] Maximization Step

Can any one suggest me how to solve this issue?

Thank you very much. Jin

[stschiff]

Hi Jin,

did you use a version not older than from a few months? Try it again with four haplotypes first. I cannot at the moment understand what's going on.

Please address me personally with these questions (stephan.schiffels@sanger.ac.uk), as long as I haven't yet set up a user forum for msmc.

Best, Stephan

On 9 Oct 2014, at 03:51, zhoujinjean notifications@github.com wrote:

Hi,

Can anyone help me with this issue?

I am running MSMC on chr1 sequencing data of 4 individuals (two individual from one population). Therefore, I have eight haploid sequences in total. I prepared the input file following the pipeline provided by msmc paper.

The command I used to run is: msmc_linux_64bit --fixedRecombination --skipAmbiguous -P 0,0,0,0,1,1,1,1 -o output input

However, the program exits without giving me a output.final.txt. I checked the log file and found that the Baumwelch iteration' Maximization Step cannot complete after 200 rounds. The log file ends with:

^M * [186/200(max)] Maximization Step^M * [187/200(max)] Maximization Step^M * [188/200(max)] Maximization Step^M * [189/200(max)] Maximization Step^M * [190/200(max)] Maximization Step^M * [191/200(max)] Maximization Step^M * [192/200(max)] Maximization Step^M^M * [193/200(max)] Maximization Step^M * [194/200(max)] Maximization Step^M * [195/200(max)] Maximization Step^M * [196/200(max)] Maximization Step^M * [197/200(max)] Maximization Step^M * [198/200(max)] Maximization Step^M * [199/200(max)] Maximization Step^M^M * [200/200(max)] Maximization Step

Can any one suggest me how to solve this issue?

Thank you very much. Jin

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